Staged-probability strategy of processing shotgun proteomic data to discover more functionally important proteins  

作　　者：Hong Xu Guijun Ma Qingqiao Tan Qiang Zhou Wen Su Rongxiu Li 

机构地区：[1]State Key Laboratory of Microbial Metabolism(Shanghai Jiao Tong University)and School of Life Sciences&Biotechnology,Shanghai Jiao Tong University,Shanghai 200240,China [2]Department of Bioinformatics and Biostatistics,College of Life Sciences&Biotechnology,Shanghai Jiao Tong University,Shanghai 200240,China [3]Software Engineering Institute,East China Normal University,Shanghai 200062,China

出　　处：《Protein & Cell》2012年第2期140-147,共8页蛋白质与细胞（英文版）

基　　金：the National S&T Major Projects of China(Key Innovative Drug Development,No.2009ZX09306-008);National Basic Research Program of China(973 Program,Grant Nos.2007CB936004 and 2009CB118906);the National Natural Science Foundation of China(Grant No.30630012);Shanghai Leading Academic Discipline Project(No.B203);Shanghai Science and Technology Innovation Action Program(Nos.072312048 and 08DZ1204400)。

摘　　要：Biologically important proteins related to membrane receptors,signal transduction,regulation,transcription,and translation are usually low in abundance and identified with low probability in mass spectroscopy(MS)-based analyses.Most valuable proteomics information on them were hitherto discarded due to the application of excessively strict data filtering for accurate identification.In this study,we present a stagedprobability strategy for assessing proteomic data for potential functionally important protein clues.MS-based protein identifications from the second(L2)and third(L3)layers of the cascade affinity fractionation using the Trans-Proteomic Pipeline software were classified into three probability stages as 1.00–0.95,0.95–0.50,and 0.50–0.20 according to their distinctive identification correctness rates(i.e.100%–95%,95%–50%,and 50%–20%,respectively).We found large data volumes and more functionally important proteins located at the previously unacceptable lower probability stages of 0.95–0.50 and 0.50–0.20 with acceptable correctness rate.More importantly,low probability proteins in L2 were verified to exist in L3.Together with some MS spectrogram examples,comparisons of protein identifications of L2 and L3 demonstrated that the stagedprobability strategy could more adequately present both quantity and quality of proteomic information,especially for researches involving biomarker discovery and novel therapeutic target screening.

关 键 词：lower minimum probability threshold probability grade TPP low-abundant protein 

分 类 号：H31[语言文字—英语]